|
| Status |
Public on Aug 31, 2018 |
| Title |
Wood_Tumor |
| Sample type |
genomic |
| |
|
| Source name |
Breast tumor tissue
|
| Organism |
Homo sapiens |
| Characteristics |
tissue of origin: Breast
clinical diagnosis: Infiltrating ductal and lobular carcinoma of the breast
ajcc/iuicc stage: IIA
|
| Treatment protocol |
None
|
| Growth protocol |
Cells were grown to reach the desired number of population doublings and extracts were harvested at 80% confluency
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cell monolayers were lysed directly in RLT+ buffer and homogenized with TissueRuptor rotor-stator homogenizer (Qiagen). Frozen tissues were homogenized by rotor-stator directly in RLT+ buffer.
|
| Label |
biotin
|
| Label protocol |
The fragemented PCR products are labeled with a single biotin at each free 3'OH using terminal deoxynucleotidyl transferase and a dideoxy biotinylated nuceloside triphosphate.
|
| |
|
| Hybridization protocol |
The biotinylated fragments are added to a hybridization solution containing a biotinylated control oligonucleotide (for quality control), and hybridized to a microarray chip overnight at 49°C.
|
| Scan protocol |
The chips are then transferred to a fluidics instrument that performs washes to remove DNA that has not hybridized to its complementary oligonucleotide probe. The bound DNA is then fluorescently labeled using phycoerythrin-conjugated streptavidin (SAPE) followed by biotinylated anti-streptavidin, followed by SAPE. Each DNA bound at its complementary oligonucleotide is excited using a confocal laser scanner, and the positions and intensitites of the fluorescent emissions are captured.
|
| Description |
Tumor used to derive Wood model
|
| Data processing |
BRLMM genotyping was performed using the Affymetrix Genotyping Console with the following parameters: Score threshold of 0.5, Prior size of 10000, DM Threshold of 0.17. Additional CEL files were added to each analysis to successfully generate prior.
The genotyping results are presented for each sample as well as the confidence values.
|
| |
|
| Submission date |
Aug 19, 2016 |
| Last update date |
Aug 31, 2018 |
| Contact name |
Elin S. Agoston |
| E-mail(s) |
esagoston@cellariabio.com
|
| Organization name |
Cellaria Biosciences
|
| Street address |
675 West Kendall Street
|
| City |
Cambridge |
| State/province |
Massachusetts |
| ZIP/Postal code |
02142 |
| Country |
USA |
| |
|
| Platform ID |
GPL3718 |
| Series (1) |
| GSE85838 |
Affymetrix SNP array data for cell line and tumor genotype alignment |
|
